1) unpack
tar -xzf rism-mol-tools_2012_10_25.tar.gz
2) go to the installation directory
cd rism-mol-tools_2012_10_25
3) compile fftw and lapack libraries ( it can take some time. If you already have lapack & fftw: just put them to libfftw3.a and lapack_LINUX.a files in the rism-mol-tools folder)
2) In the main menu select Extentions->RISM-MOL-Tools->binding
3) Fill the fields. If you are in the installation folder - you can leave all the fields untouched.
The fields:
Solute Coordinates : the solute coordinate file in *xyz or *pdb format
Solute ForceField: force-field for the solute if *ff format. The standard force field oplsaa.ff is distributed with rism-mol-tools, however it still includes only a few molecule types. you can extend the force-field if you need ( see instructions inside the oplsaa.ff file)
Solvent composition: file which describes the solvent.
Each line coresponds to one solvent component.
The first column is the name of xyz or pdb structure file.
The second column is the name of ff force-field file
Solvent RDFs: is the file which contains the RDFs of the solvent.
with rism-mol-tools only the waterRDFs.txt is distributed - the RDFs for water molecule.
the RDFs for outer solvents can be calculated using the AmberTools rism1d.
3DRISM parameters: parameters for the 3DRISM calculations. The standard file is parameters_fast.txt.
for more details see the documentation to RISM-MOL-3D program
4) push the button "Run 3DRISM". Wait 3-5 min
After the 3DRISM calculations are finished, the *distr files for each solvent component will be created.
These files contain the names of 3d distributions for each solvent component.
Select in the field "Distributions" one of these files, select the threshold to show binding molecules, and run "show binding molecules."
5) push the buttom "show Binding molecules". wait 2-3 min.
the picture like this will appear in the VMD OpenGL window
If you cannot or do not want to use the VMD, you can simply run the shell commands
The following openablefiles whill be created:
CD_in_water_water_Gmax.dx - 3d water distribution
CD_in_water_water_binding.xyz - the file with binding water molecules
RISM-MOL-Tools include:
- RISM-MOL-3D (3DRISM package)
- RISM-MOL-FF (package to assign force-fields)
- RISM-VMol (package for visualizing the binding sites)
- other useful tools, like createSlv, createOmega, 3DtoDX etc.
- VMD RISM-MOL plugin
How to Install:
0) Dowload
1) unpack
tar -xzf rism-mol-tools_2012_10_25.tar.gz
2) go to the installation directory
cd rism-mol-tools_2012_10_25
3) compile fftw and lapack libraries ( it can take some time. If you already have lapack & fftw: just put them to libfftw3.a and lapack_LINUX.a files in the rism-mol-tools folder)
./makeFFTW
./makeLAPACK
4) compile the RISM-MOL-Tools
./makeAll
5) setup paths
export PATH=$PATH:$(pwd)
echo 'export PATH=$PATH:'$(pwd) >> ~/.bashrc
(NOTE: these lines are only for bash)
6) install vmd plugin (you can get VMD at http://www.ks.uiuc.edu/Research/vmd/ )
./installVmdPlugin
How to use
VMD plugin
To test the vmd plugin:
1) in the installation folder run vmd
vmd
2) In the main menu select Extentions->RISM-MOL-Tools->binding
3) Fill the fields. If you are in the installation folder - you can leave all the fields untouched.
The fields:
Solute Coordinates : the solute coordinate file in *xyz or *pdb format
Solute ForceField: force-field for the solute if *ff format. The standard force field oplsaa.ff is distributed with rism-mol-tools, however it still includes only a few molecule types. you can extend the force-field if you need ( see instructions inside the oplsaa.ff file)
Solvent composition: file which describes the solvent.
Each line coresponds to one solvent component.
The first column is the name of xyz or pdb structure file.
The second column is the name of ff force-field file
Solvent RDFs: is the file which contains the RDFs of the solvent.
with rism-mol-tools only the waterRDFs.txt is distributed - the RDFs for water molecule.
the RDFs for outer solvents can be calculated using the AmberTools rism1d.
3DRISM parameters: parameters for the 3DRISM calculations. The standard file is parameters_fast.txt.
for more details see the documentation to RISM-MOL-3D program
4) push the button "Run 3DRISM". Wait 3-5 min
After the 3DRISM calculations are finished, the *distr files for each solvent component will be created.
These files contain the names of 3d distributions for each solvent component.
Select in the field "Distributions" one of these files, select the threshold to show binding molecules, and run "show binding molecules."
5) push the buttom "show Binding molecules". wait 2-3 min.
the picture like this will appear in the VMD OpenGL window
If you cannot or do not want to use the VMD, you can simply run the shell commands
run3DRISM solute.xyz solute.ff solvent.composition solvent.rdfs parameters.txt
runBinding distribution.distr threshold solvent.composition
(this is actually what VMD plugins do )
Example:
run3DRISM CD.xyz oplsaa.ff water.composition waterRDFs.txt parameters_fast.txt
runBinding CD_in_water_water.distr 2 water.composition
The following openablefiles whill be created:
CD_in_water_water_Gmax.dx - 3d water distribution
CD_in_water_water_binding.xyz - the file with binding water molecules